:: DESCRIPTION
G4HMM is a software of using hidden Markov models to investigate G-quadruplex motifs in genomic sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2014;15 Suppl 9:S15. doi: 10.1186/1471-2164-15-S9-S15. Epub 2014 Dec 8.
Using hidden Markov models to investigate G-quadruplex motifs in genomic sequences.
Yano M, Kato Y.
:: DESCRIPTION
qPMS9 is a parallel exact qPMS (quorum Planted Motif Search) algorithm that offers significant runtime improvements on DNA and protein datasets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
qPMS9: an efficient algorithm for quorum Planted Motif Search.
Nicolae M, Rajasekaran S.
Sci Rep. 2015 Jan 15;5:7813. doi: 10.1038/srep07813.
:: DESCRIPTION
Motus is a tool for searching and inferring reaction motifs in metabolic networks.
A metabolic network is modelled as an undirected graph. Nodes (reactions) are labelled with EC numbers (code of 4 numbers expressing the chemistry of a reaction).
A reaction motif is defined as a set of (partial) EC numbers. An occurrence of the motif in the network is a set of nodes (reactions) which is connected and labelled by EC numbers that are similar to the ones of the motif.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
V. Lacroix, C. G. Fernandes, and M.-F. Sagot.
Motif search in graphs: Application to metabolic networks.
Transactions in Computational Biology and Bioinformatics, vol. 3, pages 360-368, 2006.
:: DESCRIPTION
ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.
::DEVELOPER
Daniel GAUTHERET and André Lambert
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gautheret D, Lambert A. (2001)
Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles.
J Mol Biol. 313:1003-11
:: DESCRIPTION
A simple motif searcher. No matrices, nothing fancy, just simple searching for base strings. Allows degenerate bases to be used.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.
